The sarcomeric giants nebulin and titin both contain intragenic segmental duplication regions. Segmental duplication regions are prevalent throughout the genome and are known potential hotspots for recurrent copy number variation and may harbour pathogenic aberrations. Using our custom comparative genomic hybridization array, we have shown that gains and losses of more than one copy of the repeated block of the nebulin triplicate region are a recessive pathogenic mutation contributing to the spectrum of nemaline myopathy-causing changes. Similar copy number variants have been detected in the segmental duplication region of titin, harboured within its PEVK domain. The exact copy number determination of the segmental duplication region in titin is challenging due to the limitations of the methodology and repetitiveness of the region. We developed three complementary custom droplet digital PCR assays for the titin segmental duplication region to confirm true variation. Two of the assays target the repeated region, and one targets a diploid sequence adjacent to the segmental duplication. By comparing the data acquired by the custom comparative genomic hybridization array and the custom droplet digital PCR assays, we assessed the copy number variation of the region in 55 samples from both healthy individuals and samples from patients with different congenital muscle disorders. Our combined methods show that the titin segmental duplication region is subject to recurrent copy number variation. Gains and losses of the region were detected in both samples from healthy individuals and in samples from patients. While the copy number variation observed in our cohort is mostly unlikely to be pathogenic, it is possible that this region of titin harbours pathogenic copy number variation in a fashion similar to that of nebulin. Putative pathogenic thresholds for gains and losses remain to be studied, but the region should no longer be neglected in genetic analyses.