We analyzed the cytoplasmic diversity of CIP potato breeding germplasm. Cytoplasm types were assigned to 978 genotypes consisting of 265 foreign accessions used as input germplasm, 642 breeding lines developed by CIP, and 71 varieties released from CIP material. We found T (45 %), D (38 %), and W (11 %) to be the most frequent cytoplasm types in CIP breeding germplasm. Comparing the initial input germplasm to CIP breeding lines, the frequency of T-type cytoplasm decreased from 64 to 38 %, while those of D- and W-type cytoplasms increased from 26 to 41 % and from 6 to 14 %, respectively. We conclude that the CIP breeding program, as many others worldwide, has experienced a genetic bottleneck in terms of cytoplasmic diversity due to the unintended and continuous use of cytoplasmic-based male-sterile maternal lineages derived from Solanum demissum and S. stoloniferum in parental line and variety development. Nonetheless, the finding of male-fertile T-type breeding lines must have alleviated the problem to a certain extent, thus enabling CIP breeding progress.