We report on the methodology and first results from the Deep Lens Survey transient search. We utilize image subtraction on survey data to yield all sources of optical variability down to 24th magnitude. Images are analyzed immediately after acquisition, at the telescope and in near-real time, to allow for followup in the case of time-critical events. All classes of transients are posted to the web upon detection. Our observing strategy allows sensitivity to variability over several decades in timescale. The DLS is the first survey to classify and report all types of photometric and astrometric variability detected, including solar system objects, variable stars, supernovae, and short timescale phenomena. Three unusual optical transient events were detected, flaring on thousand-second timescales. All three events were seen in the B passband, suggesting blue color indices for the phenomena. One event (OT 20020115) is determined to be from a flaring Galactic dwarf star of spectral type dM4. From the remaining two events, we find an overall rate of eta = 1.4 events deg-2 day-1 on thousand-second timescales, with a 95% confidence limit of eta < 4.3. One of these events (OT 20010326) originated from a compact precursor in the field of galaxy cluster Abell 1836, and its nature is uncertain. For the second (OT 20030305) we find strong evidence for an extended extragalactic host. A dearth of such events in the R passband yields an upper 95% confidence limit on short timescale astronomical variability between 19.5 < R < 23.4 of eta_R < 5.2. We report also on our ensemble of astrometrically variable objects, as well as an example of photometric variability with an undetected precursor.