We created sugar-based crosslinkers for precise chemical crosslinking of atelocollagen to form a stable hydrogel microenvironment for three-dimensional (3D) cell culture. Crosslinkers were synthesized by partially oxidizing glucose, fructose, maltose, sucrose, or raffinose with periodate. The partial oxidization of sugar generated multiple aldehydes in the molecule, which acted as multifunctional crosslinkers, allowing atelocollagen to form chemical hydrogels. The crosslink reaction of atelocollagen was competitively suppressed by the addition of amino acid-rich medium, enabling flexible control of 3D molecular density in the acquired hydrogel. To evaluate structural stability, ultrasonic stress was loaded onto the acquired hydrogel and sequential mea-surement of water content showed that the crosslinking considerably stabilized the hydrogel structure. The effectiveness of the atelocollagen hydrogel as a 3D culture scaffold was analyzed by embedding and culturing endothelial cells or cardiomyocytes in it. Endothelial cells formed 3D capillary-like structures at 12 h, and cardiomyocytes formed a beating 3D netlike structure by 7 days. These findings suggest that crosslinked atelocollagen hydrogel effectively functions as a stable scaffold in 3D culture. V C 2014 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 102A: 4309-4316, 2014. How to cite this article: Kamimura W, Koyama H, Miyata T, Takato T. 2014. Sugar-based crosslinker forms a stable atelocollagen hydrogel that is a favorable microenvironment for 3D cell culture. J Biomed Mater Res Part A 2014:102A:4309-4316.