Quiescent period gating of PET data reduces respiratory motion artifacts in PET imaging. However, a respiratory phase mismatch between attenuation map and gated PET data results in PET quantitation errors particularly for lesions in the dome of the liver. To address the problem, we apply a joint estimation (JE) technique to attenuation correction for respiratory phase gated PET data. We demonstrate on clinical PET/MR data that the JE method improves PET quantitation accuracy without an additional process of respiratory phase gating of MR data. JE has additional potential to estimate patient-specific lung tissue density and provide robustness to metallic implants.