One third of type-2 diabetic patients respond poorly to metformin. Despite extensive research, the impact of genetic and non-genetic factors on long-term outcome is unknown. In this study, we combine non-linear mixed effect modeling with computational genetic methodologies to identify predictors of long-term response. 1056 patients contributed their genetic, demographic and long-term HbA1c data. The top 9 variants (of 12,000 variants in 267 candidate genes) accounted for approximately 1/3 of the variability in the disease progression parameter. Average serum creatinine level, age and weight were determinants of symptomatic response, however explaining negligible variability. Two SNPs in CSMD1 gene (rs2617102, rs2954625) and one SNP in pharmacologically relevant SLC22A2 gene (rs316009) influenced disease progression, with minor alleles leading to less and more favorable outcomes respectively. Overall, our study highlights the influence of genetic factors on long-term HbA1c response and provides a computational model, which when validated, may be used to individualize treatment.