In this study, we developed a system for detecting NPs in minute samples using affinity bead aggregation via VIF. In the proof-of-concept test using the model NP capture system with avidin-biotin interactions, the VIF caused aggregation of the capture beads only when the target NPs were present in the sample. The average area of the capture-bead aggregates, which was obtained via standard bright-field microscopy and simple image analysis, depended on the velocity of the local swirling flow induced around the micropillars, and an appropriate velocity magnitude for large aggregate formation exists. This velocity can be readily tuned using the vibration parameters such as frequency and amplitude, indicating that VIF can be applied to a wide variety of NP capture systems. Furthermore, the wide concentration range of NPs in the sample (10 7 -10 9 /ml) can be quantified from the slope of the time-dependent increase in the area of aggregates. Finally, we tested the applicability of this system for practical diagnosis using commercial EV capture microbeads. Similar to the results of the model NP capturing system, aggregation of capture beads was facilitated by VIF in a manner that enabled quantification of EV concentration.