Intellectual disability in India is substantially under-reported, especially amongst females. This study quantifies the prevalence and gender bias in household reporting of intellectual disability by estimating the age-and-gender specific prevalence of the intellectually disabled by education, Socio-Demographic Index (SDI) score, place of residence, (rural/urban) and income of household head. We estimated prevalence (per 100,000) at 179 (95% CI: 173 to 185) for males and 120 (95% CI: 115 to 125) for females. Gender differences declined sharply with increased education, was higher for lower ages and low income and varied little by state development. Under-identification and under-reporting due to stigma are two plausible reasons for the gender differences in prevalence that increase with age.