CryptosporidiumandGiardiaare major causes of diarrhoea globally, and two of the most notified infectious diseases in New Zealand. Diagnosis requires laboratory confirmation carried out mostly via antigen or microscopy-based techniques. However, these methods are increasingly being superseded by molecular techniques. Here we investigate the level of protozoa detection by molecular methods in campylobacteriosis cases missed through antigen-based assays and investigate different molecular testing protocols. We report findings from two observational studies; the first among 111 people during aCampylobacteroutbreak and the second during normal surveillance activities among 158 people presenting with diarrhoea and a positiveCampylobactertest, but negativeCryptosporidiumandGiardiaantigen-based test results. The molecular methods used for comparison were in-house end-point PCR tests targeting thegp60gene forCryptosporidiumandgdhgene forGiardia. DNA extraction was performed with and without bead-beating and comparisons with commercial real-time quantitative (qPCR) were made using clinicalCryptosporidiumpositive sample dilutions down to 10−5. TheCryptosporidiumprevalence was 9% (95% CI: 3–15; 10/111) andGiardiaprevalence 21% (95% CI: 12–29; 23/111) in the 111Campylobacteroutbreak patients. TheCryptosporidiumprevalence was 40% (95% CI: 32–48; 62/158) andGiardiaprevalence 1.3% (95% CI: 0.2–4.5; 2/158) in the 158 routine surveillance samples. Sequencing identifiedCryptosporidium hominis,C.parvum, andGiardia intestinalisassemblages A and B. We found no statistical difference in positive test results between samples using end-point PCR with or without bead-beating prior to DNA extraction, or between the in-house end-point PCR and qPCR. The qPCR Ct value was 36 (95% CI: 35–37) for 1 oocyst, suggesting a high limit of detection. In conclusion in surveillance and outbreak situations we found diagnostic serology testing underdiagnosesCryptosporidiumandGiardiacoinfections inCampylobacterpatients, suggesting the impact of protozoa infections may be underestimated through underdiagnosis using antigen-based assays.