Ameloblasts are sensitive cells whose metabolism and function may be affected by inflammatory stimuli. The aim of this study was to evaluate the possible association between polymorphisms in immune response-related genes and molar-incisor hypomineralization (MIH), and their interaction with polymorphisms in amelogenesis-related genes. DNA samples were obtained from 101 nuclear families that had at least 1 MIH-affected child. Eleven single-nucleotide polymorphisms (SNPs) were investigated in immune response genes using TaqMan® technology allele-specific probes. A transmission disequilibrium test was performed to verify overtransmission of alleles in all MIH families, as well as in families only with mild or severe MIH-affected children. Gene-gene interactions between the immune-related and amelogenesis-related polymorphisms were analyzed by determining whether alleles of those genes were transmitted from heterozygous parents more often in association than individually with MIH-affected children. In severe cases of MIH, significant results were observed for rs10733708 (<i>TGFBR1</i>, OR = 3.5, 95% CI = 1.1–10.6). Statistical evidence for gene-gene interactions between rs6654939 (<i>AMELX</i>) and the SNPs rs2070874 (<i>IL4</i>), rs2275913 (<i>IL17A</i>), rs1800872 (<i>IL10</i>), rs1800587 (<i>IL1A</i>), and rs3771300 (<i>STAT1</i>) was observed. The rs2070874 SNP (<i>IL4</i>) was also significantly overtransmitted from heterozygous parents with the rs7526319 (<i>TUFT1</i>) and the rs2355767 (<i>BMP2</i>) SNPs, suggesting a synergistic effect of the transmission of these alleles with susceptibility to MIH. This family-based study demonstrated an association between variation in <i>TGFBR1</i> and MIH. Moreover, the polymorphisms in immune response and amelogenesis genes may have an additive effect on the risk of developing MIH.