Substance exposure in utero has been associated with physical birth defects and increased risk of regulatory and neuropsychological difficulties. The aims of this study were to describe women who use substances and are in treatment with respect to the type and number of substances used during pregnancy, as well as their background, and to examine the effect substance use has on gestational age, birth weight, and the development of neonatal abstinence syndrome at birth. A sample of 161 pregnant women and their 163 newborn children were included. The results indicate that the children whose mothers continued to use substances throughout their pregnancies were born at a lower gestational age (Chi-Square = 15.1(2), P < .01); children exposed to poly-substances in utero were more affected than those exposed to only alcohol and those with no substance exposure. The same children were more vulnerable to the development of neonatal abstinence syndrome at birth (Chi-Square = 51.7(2), P < .001). Newborns who were exposed primarily to alcohol in utero were at a significant risk of being born with low birth weight (Chi-Square = 8.8(2), P < .05) compared with those exposed to other types of substances. More than 50% of the mothers ceased using any substances (with the exception of tobacco) by birth, indicating that the treatment program did have an interventional effect on the mothers. The mothers' ability to either cease or decrease the use of substances during pregnancy appears to have direct positive effect on their newborns.