Background <p>Current studies have demonstrated an association between osteoporosis (OP) and lipidome traits, yet the causal relationship between OP and lipidome remains controversial. Therefore, our aim is to explore the relationship between the lipidome and OP by calculation of genetic susceptibility.</p> Methods <p>This study utilized a two-sample Mendelian randomization (MR) approach which the instrument variables were derived from a large genome-wide database: lipidome (7174 Finnish individuals), osteoporosis (56,637 samples), fractures (426,795 samples), heel bone density (426,824 samples), whole-body bone density (56,284 samples), femoral neck bone density (32,735 samples), lumbar spine bone density (28,498 samples), and forearm bone density (8143 samples). The primary results were based on inverse variance weighting (IVW) with random effects.</p> Results <p>Based on the IVW results, we identified 138 significant associations between lipidome traits and osteoporosis and its traits (<i>P</i> &lt; 0.05). Among these, 8, 24, 27, 37, 17, 8, and 17 lipid species were significantly associated with femoral neck bone density, forearm bone density, fractures, heel bone density, lumbar spine bone density, osteoporosis, and whole-body bone density, respectively. Triglycerides were found to be significant protective factors for osteoporosis, forearm BMD, and lumbar BMD, whereas phosphatidylcholine was considered a prominent risk factor for osteoporosis, fractures, heel BMD, and lumbar BMD. The results of the heterogeneity test indicated that our IVW analysis was largely free of heterogeneity (<i>P</i> &gt; 0.05). However, the pleiotropy test revealed significant pleiotropy between heel bone density and the measurement of triacylglycerol (56:6) (<i>P</i> &lt; 0.05).</p> Conclusions <p>By applying MR methods, this study overcomes the biases inherent in traditional observational studies and provides novel mechanistic insights into lipid metabolism in op.</p> <Table Float="No" ID="Taba"> <tgroup cols="2"> <colspec align="left" colname="c1" colnum="1" /> <colspec align="left" colname="c2" colnum="2" /> <tbody> <row> <entry nameend="c2" namest="c1"> <p><b>Key Points</b></p> <p>• <i>One hundred thirty-eight significant associations found.</i></p> <p>• <i>Triglycerides protective for some bone densities, phosphatidylcholine a risk factor, phosphatidylethanolamine protective against fractures.</i></p> <p>• <i>Different lipidomic traits associated with various bone measures and fracture risk.</i></p> </entry> </row> </tbody> </tgroup> </Table>