The purpose of this paper is to study the effects of the flexibility of HDD base plates on spindle vibration via theoretical predictions and experimental measurements. The flexibility of the base plate can significantly affect HDD spindle vibration. This is the most prominent feature in 2.5 inch HDD. Nevertheless, theoretical analysis of the spindle vibration often neglects the flexibility of the non-rotating part including spindle, base plate, and top cover. Our theoretical model developed in University of Washington can include the flexibilities of spindle and base plate. As a result, our theoretical prediction generally agrees well with our experimental measurements in vibration analysis. Moreover, because of its small form factor, industrial practice is to use flanged disks instead of regular disks in vibration testing of prototypes. Our experimental measurements indicate that flanged disks and regular disks have very different behavior when the frequency is above 1 KHz.