Chilling sensitivity of maize is a strong limitation for its cultivation in the cooler areas of the northern and southern hemisphere because reduced growth in early stages impairs on later biomass accumulation. Efficient breeding for chilling tolerance is hampered by both the complex physiological response of maize to chilling temperatures and the difficulty to accurately measure chilling tolerance in the field under fluctuating climatic conditions. For this research, we used genome‐wide association (GWA) mapping to identify genes underlying chilling tolerance under both controlled and field conditions in a broad germplasm collection of 375 maize inbred lines genotyped with 56 110 single nucleotide polymorphism (SNP). We identified 19 highly significant association signals explaining between 5.7 and 52.5% of the phenotypic variance observed for early growth and chlorophyll fluorescence parameters. The allelic effect of several SNPs identified for early growth was associated with temperature and incident radiation. Candidate genes involved in ethylene signalling, brassinolide, and lignin biosynthesis were found in their vicinity. The frequent involvement of candidate genes into signalling or gene expression regulation underlines the complex response of photosynthetic performance and early growth to climatic conditions, and supports pleiotropism as a major cause of co‐locations of quantitative trait loci for these highly polygenic traits.