D. Klahr and M. Nigam (2004) make a case for the superiority of direct instruction over discovery learning in students' mastery of the control-of-variables strategy central to the scientific method. In the present work, we examine acquisition of this strategy among students of the same age as those studied by Klahr and Nigam, as well as follow central features of their design in directly comparing the two methods. In contrast to their design, however, we follow progress over an extended time period and a range of equivalent tasks. Three groups of 15 fourth-grade students, of diverse socioeconomic background, were compared. One group engaged in 12 sessions over 10 weeks working on problems that required the control-of-variables strategy for effective solution. Another group engaged in the same activity, preceded by a session involving direct instruction on the control-of-variables strategy. A third group received only the initial direct instruction, without subsequent engagement and practice. In this longer term framework, direct instruction appears to be neither a necessary nor sufficient condition for robust acquisition or for maintenance over time. The patterns of attainment observed here point instead to a gradual and extended process of acquisition and consolidation. © 2006 Wiley Periodicals, Inc. Sci Ed91:384–397, 2007