Genetic variations and their relationships to individual fitness have been the major topics in studies of ecology and evolution. The concept that a reduction in genetic variations leads to lower fecundity termed “inbreeding depression” has been predominantly supported by studies involving laboratory organisms, but has rarely been tested in wild populations. We therefore examined whether the individual genetic diversity among a population of wild sika deer (Cervus nippon) on Kinkazan Island, northern Japan, affected neonatal weight that is often considered as a fitness-related trait. First, the neonatal weights of fawns born during 1994–2004 were recorded, and 11 microsatellite loci were genotyped to obtain 5 different estimates of an individual's genetic diversity. To test whether the genetic diversities of fawns correlated with their neonatal weights, multivariate analyses using a generalized linear mixed model were performed. The neonatal weights were significantly affected by standardized multilocus heterozygosity and mother's body condition, as well as the interaction of these factors. Interestingly, the model indicated that neonatal weight was positively correlated with the genetic diversities of fawns only when the mothers' body weight exceeded a certain level that varies according to their reproductive history.