Estrogen receptor (ER) status is an important biomarker in defining subtypes of breast cancer differing in antihormonal therapy response, risk factors and prognosis. However, little is known about association of ER status with various risk factors in the developing world. Our case-control study done in Kerala, India looked at the associations of ER status and risk factors of breast cancer. From 2002 to 2005, 1,208 cases and controls were selected at the Regional Cancer Center (RCC), Trivandrum, Kerala, India. Information was collected using a standardized questionnaire, and 3-way analyses compared ER+/ER- cases, ER+ cases/controls and ER- cases/controls using unconditional logistic regression to calculate odds ratios and 95% confidence intervals. The proportion of ER- cases was higher (64.1%) than ER+ cases. Muslim women were more likely to have ER- breast cancer compared to Hindus (OR = 1.48, 95% CI = 1.09, 2.02), an effect limited to premenopausal group (OR = 1.87, 95% CI = 1.26, 2.77). Women with higher socioeconomic status were more likely to have ER+ breast cancer (OR = 1.48, 95% CI = 1.11, 1.98). Increasing BMI increased likelihood of ER- breast cancer in premenopausal women (p for trend < 0.001). Increasing age of marriage was positively associated with both ER+ and ER- breast cancer. Increased breastfeeding and physical activity were in general protective for both ER+ and ER- breast cancer. The findings of our study are significant in further understanding the relationship of ER status and risk factors of breast cancer in the context of the Indian subcontinent.