Fruit morphology is one of the most important traits in cucumber because it directly affects its commercial value. The cucumber line CS-PMR1 is a promising breeding material for improving disease resistance, but its fruit morphology is not ideal for the Japanese market, and this hampers breeding. We used recombinant inbred lines derived from a cross between CS-PMR1 and the Japanese cultivar 'Santou' for genetic analysis of fruit morphological traits. Fruit shape variation was evaluated in detail by means of image analysis, and quantitative trait locus (QTL) analyses were performed by composite interval mapping or interval mapping with a nonparametric model. We detected 41 QTLs: 5 for length, 6 for diameter, 5 for the ratio of length to diameter, 4 for the ratio of placenta diameter to fruit diameter, 16 for principal component scores of elliptic Fourier descriptors related to fruit shape, 2 for wart size and 3 for wart density. Some QTLs were detected in the same chromosomal regions at different fruit stages and for different morphological traits. In particular, several QTLs with large effects on fruit size were located in nearly the same regions as genes for resistance to powdery mildew and downy mildew, indicating that the linkage between fruit shape and the resistance genes is likely to limit breeding efficiency. The results of this study will contribute to the development of informative DNA markers tightly linked to genes for requisite fruit morphological traits, which are urgently required for efficient breeding of new cultivars.