Health traits are regarded extremely important in cattle breeding with high economic value and a very low heritability. In this study, a medium density SNP chip (54,001 SNPs) was used to investigate the genomes of 7,404 Fleckvieh bulls to identify chromosomal regions associated with different functional traits, such as calving ease, stillbirth, fertility and length of productive life. The analysed data set consisted of 41,889 autosomal SNPs after quality control and 5,673 to 7,384 animals depending on the trait combination. The main tool for the analysis of pleiotropic effects was the CAPE software package in R. This tool implements a method indicating directed interaction networks between genetic variants for predicting the influence of genetic interference on phenotypes. Several pleiotropic regions were detected for each of the six trait pairs, the most for calving ease and longevity (11 regions on seven chromosomes), the least for stillbirth and fertility (four regions on two chromosomes). Regions around 9.8Mb, 23-24Mb, 27Mb on BTA14, 17.5Mb on BTA 17 and 2-3Mb on BTA 21 were detected in multiple trait pairs, with the most prominent representation of BTA 14 in all but one trait pair (fertility-longevity). Genomic regions with multiple occurrences are hypothesized to have special importance in functional traits, containing genes influencing neural development (KCNQ3), growth and birth weight (XKR4, LYN, SOX17, PLAG1 and others), spermatogenesis and fertility (CLGN), immune response (ELMOD2), thermoregulation (UCP1 and TBC1D9) and fetal growth (UBE3A). The direction of the effects was the same for most pleiotropic regions, although there were also cases of antagonistic relationships between traits. This study helps to explain the genetic architecture for different functional traits in Fleckvieh cattle, and it provides useful information for breeding organisations and for future work on the topic pleiotropy in cattle.