The Veterans Health Administration (VA) is one of the largest providers of care to transgender people in the US and the VA’s national electronic health record (EHR) can help providers identify need for cancer screens. However because current functionality in the EHR allows but does not document overwriting sex of record to reflect self-identified gender identity, sex-specific warranted care cannot be determined. To illustrate this problem, we explored rates of cervical and prostate cancer screenings by sex of record for veterans in VA care with and without gender-related diagnoses. Between 2009 and 2019, 8,454 veterans with at least one gender-related diagnostic code were matched 1:2 on age, race, ethnicity, and VA facility to veterans without these codes (N = 16,901). Among veterans with a gender-related diagnosis, rates of cervical cancer screening for those with a sex of record as female were substantially lower than sex-of-record female veterans without a gender-related diagnosis. Veterans with sex-of-record as male were substantially more likely to have received a cervical cancer screening than sex-of-record male veterans without a gender-related diagnosis. Rates of PSA testing among Veterans with a gender-related diagnosis were higher than among veterans without a gender-related diagnosis, regardless of sex of record. Observed differences in rates reflect the disconnect that results between EHR-documented sex-of-record and sex-specific care when original sex of record is overwritten. Implications include the need to utilize an organ inventory and create a new variable in EHR reflecting self-identified gender.