The purpose of this study was to compare the effects of two different methods of organizing endurance training in trained cyclists during a 12-week preparation period. One group of cyclists performed block periodization (BP; n = 8), wherein every fourth week constituted five sessions of high-intensity aerobic training (HIT), followed by 3 weeks of one HIT session. Another group performed a more traditional organization (TRAD; n = 7), with 12 weeks of two weekly HIT sessions. The HIT was interspersed with low-intensity training (LIT) so that similar total volumes of both HIT and LIT were performed in the two groups. BP achieved a larger relative improvement in VO2max than TRAD (8.8 ± 5.9% vs 3.7 ± 2.9%, respectively, P < 0.05) and a tendency toward larger increase in power output at 2 mmol/L [la−] (22 ± 14% vs 10 ± 7%, respectively, P = 0.054). Mean effect size (ES) of the relative improvement in VO2max, power output at 2 mmol/L [la−], hemoglobin mass, and mean power output during 40-min all-out trial revealed moderate superior effects of BP compared with TRAD training (ES range was 0.62–1.12). The present study suggests that BP of endurance training has superior effects on several endurance and performance indices compared with TRAD.