Diagnosis of periodontal disease progression involves recording two probing attachment level measurements over an adequate time interval. A diagnostic instrument which exhibits less measurement variability allows for increased sensitivity and earlier disease detection. Traditionally, a manual probe with an occlusal stent of the cementoenamel junction (CEJ) as a reference landmark has been the method of choice. Automated probes that use an occlusal disk as the reference landmark have been developed as an alternative means of measure. The aim of this study was to compare the variability of these two probing methods. Four hundred eleven (411) interproximal sites in 46 untreated periodontitis patients were monitored by a single examiner over a 6-month period. Each site was measured on a monthly basis, first with an automated probe (AP) followed by a manual probe (MP) in combination with a custom-fabricated acrylic stent. Measurement variability of the two probing methods was also compared over a 7-day interval. The AP measurements were significantly more variable than the MP measurements (P < 0.001) when considering the variability between two passes at the same visit. Over the 6-month period, the MP measurements demonstrated significantly more variability than the AP measurements (P < 0.001). It was also noted that MP measurements exhibited more variability at sites with frequent bleeding during the 6 months of the study (P = 0.006). The results of this study demonstrate that AP may have less variability of attachment level measurements over a 6-month period and may be less influenced by local inflammatory changes. However, future comparison studies should include multiple examiners to reduce examiner bias and should alternate the probing method to reduce bias created by local tissue changes from multiple probings.