Mutants often reduce fitness when incorporated into some genotypes, as is the case of the mutant gene sugary1 (su1) in maize (Zea mays L.). Understanding the genetic factors affecting variation in the fitness of a mutant is of major interest from a theoretical point of view and also from a breeder's perspective. The genetic regulation of su1 behaviour was examined in two independent materials. First, populations of two recombinant inbred lines (RIL) were used, belonging to the Nested Association Mapping (NAM) design produced from crosses between the maize inbred B73 and two sweet corn lines (P39 and Il14h) that were genotyped with 1106 single nucleotide polymorphisms (SNPs). These RILs had a group of lines with the su1 allele and another group with the wild allele. At each marker, the allele frequencies of both groups of RILs were compared. Second, an F2 population derived from the cross between A619 (a field maize inbred line) and P39 (a sweet corn inbred line) was characterized with 295 simple sequence repeats (SSRs). In addition, the population was phenotyped for several traits related to viability. A large linkage block was detected around su1 in the RILs belonging to the NAM. Furthermore, significant genomic regions associated with su1 fitness were detected along the 10 maize chromosomes, although the detected effects were small. Quantitative trait loci (QTLs) with effects in multiple traits related to su1 fitness were detected in the F2 population, for example at bin 5·04. Therefore, the present results suggest that the su1 fitness depends on many genes of small effect distributed along the genome, with pleiotropic effects on multiple traits.