BACKGROUND: This study analyses whether a mother's exposure to different forms of Intimate Partner Violence (IPV) during pregnancy was associated with the index child linear growth, and whether these associations were modified by the gender of the child. METHODS: A pregnancy cohort of 478 women in León, Nicaragua, resulted in 461 live births. From this group, 81% (375/461) children were available for anthropometric follow-up at 40 to 46 months. Analysis of covariance (ANCOVA) was used to assess the association between IPV and height-for-age Z-scores, adjusting for confounding factors. RESULTS: Sixty-three percent (236/375) of the mothers had been exposed to some form of IPV during pregnancy (emotional, physical, sexual or controlling behavior). After adjustment for confounding factors, maternal exposure to any IPV during pregnancy was associated with 0.24 lower mean height-for-age Z-scores (p = 0.02). A separate analysis of each IPV type showed that emotional, physical or sexual IPV during pregnancy were not significantly associated with lower mean height-for-age Z-scores, whereas ever exposure to controlling behavior by the father of the child was related to 0.29 lower mean height-for-age Z-scores (p < 0.01) When stratified by gender, these associations remained significant only for young girls. CONCLUSIONS: This study has contributed to the growing amount of evidence pointing to the pervasive effect of different forms of IPV on child health. Our study highlights the relevance of maternal autonomy for linear child growth, especially for young girls in the Nicaraguan context.