The use of a specific antibody conjugated with nanobeads, forming immunomagnetic nanobeads (IMNBs), has been demonstrated to be useful for the capture and detection of viruses. In this study, IMNBs functionalized with a single-domain antibody against the capsid protein (Cap) of porcine circovirus type 2 (PCV2), hereafter denoted as psdAb, were evaluated and used to capture PCV2. Quantum dots (QDs) conjugated with psdAb were used as a fluorescence probe to visualize PCV2 captured by IMNBs. The specificity and sensitivity of this method were further evaluated using common pathogens of pig viral disease and PCV2. To assess its practicality, clinical samples were tested in this study. The results showed that 2.57 ± 0.13 mg Cap or 0.97 ± 0.064 × 10(6) copies of PCV2 particles could be captured by 1 mg of IMNBs in 30 min. This suggests that the IMNBs have the ability to efficiently capture PCV2 with good specificity, as there was no cross-reaction with other pathogens, and with strong sensitivity, with a detection limit as low as 10(3) copies/ml of PCV2 particles. Moreover, PCV2 in inguinal lymph node, lung, spleen, serum, and fecal samples was successfully detected by IMNBs. The results demonstrate that this method is promising for the rapid and effective detection of PCV2 in complex clinical samples.