This study investigated in vivo degradation of Ti-6Al-4V alloy miniscrew implants. Miniscrew implants were placed in patients, and the surfaces were studied upon retrieval by scanning electron microscopy, microscale X-ray photoelectron spectroscopy, elastic recoil detection analysis and nanoindentation testing. Bone-like structures were formed on the retrieved specimens. The hardness and elastic modulus of the surfaces of the retrieved specimens were significantly lower than the as-received specimens, although no statistically significant differences were observed for the hardness and elastic modulus in the bulk region. Thick organic over-layer containing carbon, oxygen, and nitrogen, with the thickness greater than 50 nm, covered the retrieved specimens, and higher concentrations of hydrogen were detected in the retrieved specimens compared with the as-received specimens. Minimal degradation of the bulk mechanical properties of miniscrew implants was observed after clinical use, although precipitation of bone-like structures, formation of a carbonaceous contamination layer, and hydrogen absorption were observed on the surfaces of miniscrew implants.