To investigate the relationship between anthropometric, biochemical, and hematologic parameters and serum leptin and homocysteine (Hcy) levels. Also, to determine the effect of leptin and Hcy on expression of genes associated with cardiovascular disease susceptibility (APOA1, LRP1, COX-1, and COX-2) in mononuclear cells of healthy pregnant women. Between August 2018 and January 2020, a cross-sectional study was conducted on 161 healthy pregnant women in Tabasco, southeastern Mexico. The study population was classified by trimester, according to gestational pregnancy. Anthropometric, biochemical (leptin and homocysteine), and hematologic data were obtained under fasting conditions. APOA1, LRP1, COX-1, and COX-2 expression in mononuclear cells was evaluated using RT-qPCR. Red cell indices (hemoglobin, hematocrit, and erythrocytes) were negatively and positively correlated with leptin and Hcy levels, respectively, in the first- and second-trimester groups. Increased leptin levels and low red cell indices were significantly associated with BMI <25.0 in the second-trimester group; however, no significant differences were observed in Hcy levels. Increased leptin and Hcy levels were significantly associated with high lipid indicators in the first- and third-trimester groups, respectively. High APOA1 and COX-2 expression was significantly associated with reduced leptin and increased Hcy levels in the second- and third-trimester groups. Increased leptin and Hcy levels during pregnancy, mainly associated with modifications in erythrocytes and lipid indices, may lead to early modification of genes related to lipid metabolism (APOA1) and proinflammatory response (COX-2) and, thereby, increase cardiovascular disease risk.