The rind penetrometer is an effective tool for measuring stalk strength in an effort to improve maize (Zea mays L.) germplasm for stalk lodging resistance. However, previous studies have indicated a significant negative correlation between rind penetrometer resistance (RPR) and ear height (EH). The correlation between RPR and EH is of interest in understanding response to selection for RPR. Has selection for high RPR resulted primarily in increased stalk strength per se and coincidentally lower ear heights, or has selection for high RPR resulted in lower ear heights and subsequently higher stalk strength? The objective of this study was to determine the genetic relationship between RPR and the correlated trait EH. To accomplish this goal, three F2:3 populations were used to characterize and compare quantitative trait loci (QTL) for RPR, EH, and RPR adjusted for EH (RadjE). The original QTL analysis of RPR detected a total of 26 QTL across populations. Adjusting RPR for EH caused 11 of the original RPR QTL to lose their significance. However, the majority, 15 of 26, of the original RPR QTL remained significant as QTL for RadjE. Because EH clearly had an effect on RPR, adjusting RPR for EH likely resulted in more accurate descriptions of QTL for stalk strength per se. We have demonstrated that QTL analysis can be used to separate the effects of correlated traits from the genetic effects of the trait of interest, and recommend determining which correlated traits may influence measurement of the main trait before initiating a QTL experiment.