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The Encyclopedia on Early Childhood Development says:

However, the evidence from literature on both animals and humans is very convincing: smoking during pregnancy is a contributing factor to a host of short- and long-term effects on the growth and neurobehavioural development of offspring.

Other studies contradict these results:

the associations between maternal smoking and 12 other outcomes studied (including Apgar score, intelligence, academic achievement, conduct problems, and asthma) were entirely eliminated after adjustment for measured and unmeasured confounders. The authors conclude that the hypothesized effects from maternal smoking during pregnancy on these outcomes either are not present or are not distinguishable from a broader range of familial factors associated with maternal smoking. — Maternal Smoking...

Unadjusted analyses showed a statistically significant decrement of 4 points on full-scale IQ (FSIQ) associated with smoking 10+ cigarettes per day compared to nonsmoking. After adjustment for potential confounders, no significant effects of prenatal exposure to tobacco smoking were found. Considering the indisputable teratogenic effects of tobacco smoking, these findings should be interpreted with caution. Still, the results may indicate that previous studies that failed to control for important confounders, particularly maternal intelligence, may be subject to substantial residual confounding. — Effects of ...

Wikipedia's page on confounders:

In risk assessments, factors such as age, gender, and educational levels often have an impact on health status and so should be controlled. Beyond these factors, researchers may not consider or have access to data on other causal factors. An example is on the study of smoking tobacco on human health. Smoking, drinking alcohol, and diet are lifestyle activities that are related. A risk assessment that looks at the effects of smoking but does not control for education, alcohol consumption or diet may overestimate the risk of smoking.

Yet, after removing this bias (for example with enough data available it's possible to cohort similar classes of mothers), I found there some significant measures could be found on mental retardation:

Smoking has been linked to small cognitive, achievement, and behavioral deficits but has not been associated with more severe cognitive impairments. This investigation evaluated the relationship between maternal smoking during pregnancy and idiopathic mental retardation
Data on maternal smoking during pregnancy were obtained during face-to-face interviews with the mothers of 221 children with idiopathic MR and the mothers of 400 children attending public school. All children had been born in the five-county metropolitan Atlanta area in 1975 or 1976 and were living in the area when they were 10 years of age. We used exposure odds ratios (ORs) to assess the relationship between maternal smoking and MR, controlling for sex, maternal age at delivery, race, maternal education, economic status, parity, and alcohol use.
Maternal smoking during pregnancy was associated with slightly more than a 50% increase in the prevalence of idiopathic MR (adjusted OR, 1.6; 95% confidence interval, 1.0-2.4), and children whose mothers smoked at least one pack a day during pregnancy had more than a 75% increase in the occurrence of idiopathic MR (OR, 1.9; 95% confidence interval, 1.0-3.4). This increase was neither accounted for by other sociodemographic risk factors for MR nor explained by an increase in the prevalence of low birth weight among the children of smokers.
Our data suggest that maternal smoking may be a preventable cause of mental retardation.

However mental retardation is an extreme case, which is probably not proportional or related with the others possible harms and effect that this question asks.
After seeing those contradictories claims, the original question remains unclear. Can we prove that for similar environmental factors, a mother smoking behaviour (more than 10/day vs non-smoker) during pregnancy will affect significantly the child's development process, his capacity to learn?

Are the proven geno/cyto-toxicity of tobacco toxins responsible for an intellectual deficit since it would affect lifelong* or very long-term cells like neurons and reduce neurogenesis?

lifelong* (edit from comment)

It has been demonstrated that neurogenesis can sometimes occur in the adult vertebrate brain, a finding that led to controversy in 1999.[30] However, more recent studies of the age of human neurons suggest that this process occurs only for a minority of cells, and the overwhelming majority of neurons comprising the neocortex were formed before birth and persist without replacement.

edit: other relevant indicators:

Nicotine targets specific neurotransmitter receptors in the fetal brain, eliciting abnormalities of cell proliferation and differentiation, leading to shortfalls in the number of cells and eventually to altered synaptic activity. — Fetal nicotine...

addendum: This study seems to answer the question, however the full pdf isn't available for free

  • Note: I made a substantial edit that, in particular, reversed what you claimed the second study showed. Please check it still matches your question. – Oddthinking May 8 '14 at 2:52
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    "which may affect lifelong cells like neurons" - please provide a reference for the effect, and that neurons are "lifelong". – user5582 May 8 '14 at 15:46
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    It is unclear what you are asking here. This post has becoming a literature review, not a question. – Oddthinking Jul 8 '14 at 9:25
  • the idea was to understand if prenatal smoking could cause a proportional harm to the baby, throughout his life, by altering permanently a part of its vital functions (stem cells, neurogenesis), and didn't find the answer precise enough on this – caub Jul 8 '14 at 11:34
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+100

The CDC, NIH, Mayo Clinic, ACS, ALA, and the Australian Government are all saying the same thing. There are known studies that smoking lowers the birth-weight of a baby, which is one of the main factors in their likelihood to survive. It also raises the risk of SIDS.

According to Laws PJ, Grayson N & Sullivan EA babies of smoking mothers are 50% more likely to be stillborn and twice as likely to be low birth weight than babies born to nonsmoking mothers.

I haven't found any evidence to imply that smoking has a positive or neutral effect on babies health.

Edit:
I found this article showing the chemicals in tobacco smoke that are known to cause damage. This article on the same site explains that the chemicals travel through the mother's bloodstream and enter the baby giving the baby exposure to the same chemicals. It also shows some of the effects tobacco can have to developing babies.

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