Different autoantibodies are often measured simultaneously; this typically occurs when using indirect immunofluorescence on tissue sections or multiplex detection systems and may generate clinically "unexpected" positivities (i.e., without any relation to the disease under investigation). Their number is expected to increase with the development of microarray systems in autoantibody assays. In general, when examining patients with such unexpected findings, it is necessary to take into account that: a) autoantibody positivities are much more frequent than autoimmune diseases; b) the positive predictive value of an autoantibody positivity depends upon the diagnostic accuracy of the test and disease prevalence; c) autoantibodies may be risk factors for autoimmune disease or may also have a pathogenetic role by themselves. In this article we will highlight the possible problems raised by some relatively common situations, related to anti-nuclear, anti-thyroid, anti-phospholipid and anti-tissue transglutaminase autoantibodies. The need for specific strategies is outlined.