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Rationale: Clumped isotope (Δ47) analysis of bioapatite‐derived CO2 is a powerful tool to determine body temperatures of extinct vertebrates. The common acid bath technique in combination with dual‐inlet‐based mass spectrometric measurements has been the preferred method of choice for this purpose, but the large amount of material necessary and the presence of secondary calcite represent obstacles. Methods: We analyzed the Δ47 composition of carbonate‐bearing (bio)apatites using a Kiel IV device, which – in general – allows a reduction of sample replicate size by a factor of ~40 over dual‐inlet‐based techniques. The Kiel IV device was tested in two different modes: without and with additional water sinks for improved water removal. Furthermore, we tested a pretreatment technique based on 1 M acetic acid (pH = 5) to selectively remove secondary calcite from the carbonate‐bearing (bio)apatite phase. Results: Significantly lower Δ47 values were obtained for a given bioapatite after the installation of the two water sinks. With this setup, Δ47 of (bio)apatites followed a temperature relationship that is indistinguishable from the unified one for pure carbonates, provided a dentine sample, rich in organic matter, was excluded. The original bioapatite Δ47 value was restored from a bioapatite/calcite mixture if the mixed material was treated for 1 h with 1 M acetic acid (pH = 5). Conclusions: (Bio)apatites having low organic matter content such as enamel(oid) can be analyzed accurately for Δ47 using a Kiel IV equipped with water sinks that ensure effective removal of water. Secondary calcite can be effectively removed from carbonate‐bearing apatite by pretreatment with 1 M acetic acid (pH = 5) for 1 h. [ABSTRACT FROM AUTHOR] more...