I know that %r in logback outputs the relative time from the start of the logging event in milliseconds, but it seems that there's not way to set it in a pattern like HH.mm.ss.SSS.

Unfortunately, something along the lines of %r{HH.mm.ss.SSS} (which is the way I do it for the current date/time %d) doesn't work. I can of course build a StopWatch object and manually output its value every time I call the logger, but this way seems rather unpractical.

Such a feature would be quite useful I think, and I was also suggested to post a feature request here after asking a similar question on stackoverflow.