Abstract Background Valproic acid (VPA) exposure in utero has been associated with an increased risk of both neural tube defects and autism spectrum disorders (ASDs). The terata induced by VPA suggest interference with pattern formation. Retinoic acid produces similar terata and is known to act in part by increasing the expression of Hoxa1. We tested the hypotheses that exposure to VPA would alter the expression of Hoxa1 in rat embryos during times of normal Hoxa1 expression (d10.5–13.5) and that exposure at earlier and later stages would induce inappropriate expression. Method Hoxa1 expression levels were determined by real-time PCR in individual embryos 1 h after exposure on gestational d10, 12, 13, 14, or 15. Additionally, teratogenic (4- yn-VPA) and nonteratogenic analogs of VPA (IE-VPA), retinoic acid (RA), and saline were compared for effects on Hoxa1 expression on d12. Embryos were allowed to develop for 1, 2, 4, 6, or 24 h, to follow the time course of effects. Results In utero exposure to VPA on gestational d10 and on d12–14 significantly increased the level of Hoxa1 expression compared to saline-exposed embryos at developmental ages prior to, during and after the normal expression period for this gene. On gestational d12, exposures to VPA and 4- yn-VPA significantly increased Hoxa1 expression at all sacrifice times, compared to saline-exposed embryos. RA significantly elevated Hoxa1 expression at all time points except 24-h post-treatment. The nonteratogenic VPA analog, IE-VPA, did not affect Hoxa1 expression. Conclusions VPA and 4- yn-VPA exposures elevated Hoxa1 mRNA during its normal expression period and induced expression outside of the normal period. This may explain, in part, how VPA disrupts development.