We have studied the petrochemistry of degraded bones and sediment from the interior of four ossuaries (burial boxes) discovered in what is (arguably) believed to be the 1st century CE family tomb of the high priest Caiaphas (herewith Cft) in Jerusalem. During the course of the 1990 excavation, among other artifacts (e.g., a coin found in a skull) two iron nails were discovered. One of the nails was inside an ossuary, the other on the floor of one of the nearby “kokhim” (burial niches) which contained Ossuaries 5 and 6. According to the Israel Antiquities Authority (IAA) everything in the burial cave can be accounted for today except the iron nails “which have been misplaced”, this without being properly recorded or photographed. Investigative journalist Simcha Jacobovici believes that he has located the nails in the artifacts collection of the Anthropology laboratory at Tel Aviv University. The IAA, however, has stated that the lost nails from the Cft have nothing to do with the nails found at the university and the latter nails must have a different provenance. Wherever lies the truth, the presence of two nails in the Cft is of profound interest because in the New Testament the high priest Caiaphas was responsible for passing Jesus to the Romans who then sent him to the cross. The possibility that the nails were used in a crucifixion on the one hand and can be connected to Caiaphas the high priest on the other is, to say the least, interesting and potentially monumental. Aware of the controversy but also of the importance of the two unprovenanced nails we have investigated the materials which have invaded the interiors of the Cft ossuaries and in a similar manner materials that have adhered to the two unprovenanced nails. Employing geochemical and petrochemical Scanning Electron Microscope (SEM-EDX), X-ray diffraction (XRD) and δ18O and δ13C isotope analyses we have found that the organic and inorganic materials flushed into the interior of the Cft but also those that have adhered to the two unprovenanced nails possess and display many identical, and what can also be termed unique chemical and physical characteristics. Based on the collective evidence we conclude, with considerable confidence, that the unprovenanced nails are the lost nails excavated from the Caiaphas family tomb in 1990 and furthermore that these nails were used in a crucifixion.