Failure to grow (ill-thrift) in calves has a negative effect on animal production and health. The present study was carried out from November, 2009 to May, 2013 to investigate the risk factors of ill-thrift in buffalo calves. A total of 344 calves at 78 smallholder farms were selected randomly. A questionnaire was designed to include managemental, nutritional and disease risk factors. Serum selenium, copper, zinc, iron, calcium, phosphorus and magnesium were measured. Data were subjected to logistic regression analysis and results were expressed as p value, odds ratio (OR) and confidence interval (CI). Fifty-five calves (15.9%) showed ill-thrift. On animal level, the final multivariate logistic regression model showed a significant association between ill-thrift and early weaning (p < 0.01; OR: 45.755; CI: 4.35–480.25), diarrhea (p < 0.05; OR: 41.315; CI: 1.710–998.0), indoor management (p < 0.05; OR: 63.56; CI: 2.701–14.96) and low serum phosphorus (p < 0.01; 292.0; CI: 5.256–16.23). On farm level, inadequate mineral supplementation (p < 0.001; OR: 18.62; CI: 3.89–88.9) and irregular use of anthelmintics (p < 0.05; OR: 7.95; CI: 1.53–41.23) were the potential factors. Clinically, ill-thrift calves were more likely to have alopecia (p < 0.01), recumbency (p < 0.01), emaciation (p < 0.001), hypothermia (p < 0.01), inappetance (p < 0.001), lacrimation (p < 0.001), hypomotile rumen (p < 0.001), and pale mucous membrane (p < 0.001). The results of the present study indicate that ill-thrift in buffalo calves could occur as a result of interaction between management errors and disease factors. Identification of the risk factors associated with ill-thrift may provide useful information, which assist to construct the suitable preventive measures.