Serotonin (5-HT) is a widely studied neurotransmitter which plays an important role in the development and proper functioning of the organism throughout life. The appearance of 5-HT system early in ontogeny suggests the hypothesis that 5-HT plays a regulatory role in neurodevelopment. This study investigated the effect of administration of a tryptophan deficient diet during prenatal development on the morphology and cell population of the dorsal raphe. The experimental diet, containing balanced amounts of carbohydrates, lipids and proteins, was provided to a time-mated group of rats from gestational day 5 until delivery. Control groups were fed with (i) the experimental diet formulation with 0.2% tryptophan added to the mixture, or (ii) a regular chow diet. At delivery, five pups per dam were euthanized. Body and brain weight was measured and brain sections were processed for immunohistochemistry for tryptophan hydroxylase (TrpH) and whole brain 5-HT analysis. Sections containing dorsal raphe were photographed with a light microscope and TrpH positive neurons quantified. Brain weights in the tryptophan deprived group showed no difference as compared with controls while body weights were reduced by 25%. Total numbers of serotonergic neurons at the dorsal raphe in the prenatal tryptophan deficient pups were reduced by 35%. A regional analysis of the dorsal raphe indicated a marked cellular reduction in the medial and caudal sections of the nucleus, which contains the majority of serotonergic neurons, in the tryptophan deprived condition. Quantitative 5-HT analysis showed that the brain concentration was similar among conditions. In conclusion, gestational tryptophan deprivation exerts adverse effects on the development of the 5-HT system, particularly in the dorsal raphe, manifested by decreased numbers of serotonergic neurons as well as altered topography in this important nucleus. (C) 2012 ISDN. Published by Elsevier Ltd. All rights reserved.