The purpose of this study was to demonstrate the feasibility of accurate quantification in pinhole SPECT using micro-CT information. Pinhole SPECT scans were performed using a clinical dual-head gamma camera. Each pinhole SPECT scan was followed by a micro-CT acquisition. Functional and anatomical images were coregistered using six point sources visible with both modalities. Pinhole SPECT images were reconstructed iteratively. Attenuation correction was based on micro-CT information. Scatter correction was based on dual and triple-energy window methods. Phantom and animal experiments were performed. A phantom containing nine vials was filled with different concentrations of (99m)Tc. Three vials were also filled with CT contrast agent to increase attenuation. Activity concentrations measured on the pinhole SPECT images were compared with activity concentrations measured by the dose calibrator. In addition, 11 mice were injected with (99m)Tc-labelled Nanobodies. After acquiring functional and anatomical images, the animals were killed and the liver activity was measured using a gamma-counter. Activity concentrations measured on the reconstructed images were compared with activity concentrations measured with the gamma counter. The phantom experiments demonstrated an average error of -27.3 +/- 15.9% between the activity concentrations measured on the uncorrected pinhole SPECT images and in the dose calibrator. This error decreased significantly to -0.1 +/- 7.3% when corrections were applied for nonuniform attenuation and scatter. The animal experiment revealed an average error of -18.4 +/- 11.9% between the activity concentrations measured on the uncorrected pinhole SPECT images and measured with the gamma counter. This error decreased to -7.9 +/- 10.4% when attenuation and scatter correction was applied. Attenuation correction obtained from micro-CT data in combination with scatter correction allows accurate quantification in pinhole SPECT.