We performed three-dimensional detection of magnetic nanoparticle (MNP) samples using the combination of a field-free line (FFL) and multiple pickup coils. In this method, two-dimensional maps of the signal fields generated by the MNP samples were used to reconstruct a threedimensional image of the MNP concentration. In the experiment, a weak field gradient of the FFL (0.06-0.13 T m −1 ) was used. The degradation of the imaging quality owing to the weak field gradient was compensated using ten field maps. We successfully demonstrated the three-dimensional detection of two MNP samples. The Fe content of each sample was 10 and 20 μg and the spacing for both samples was 16 mm. The results confirm the effectiveness of the present method for MNP detection using a weak field gradient. We also quantitatively discuss how the imaging quality degrades when the field gradient is decreased.