A microchip in which a flow channel groove is formed in a surface of at least one of two resin substrates (10, 20); the two resin substrates (10, 20) are joined with a face facing inward where the flow channel groove is formed; in at least either one of the two resin substrates a through-hole of a circularly cross-sectional shape leading to the flow channel groove from a face of an opposite side to the face where the two resin substrates are joined is formed; and a space is formed in a joint face of the resin substrates in which the flow channel groove has been formed in one of the two resin substrates and the space has a depth (Tc) so as for a clearance to remain between the tip side edge of the through-hole and the joint face even when the two resin substrates (10, 20) are joined, in the face of the opposite side, a protrusion protruding in a thickness direction of the resin substrate is integrally formed with the resin substrate so as to surround the through-hole, characterized in that, the microchip in which the space having a circularly cross-sectional shape concentric with the through-hole and the depth in the same direction as the thickness direction of the resin substrate is formed on the joint face of at least one of the two resin substrates which is the joint face in the case where the protrusion is projected from a perpendicular direction to the joint face, when the tip side edge of the through-hole is projected on the joint face from the perpendicular direction, a relationship of φc > φa is satisfied and φa is larger than a width of the flow channel groove, provided that the diameter of the tip side edge of the through-hole is designated as φa and the diameter of the end edge side of the space making contact with the joint face is designated as φc, wherein the space has a peripheral wall face slanting from the end edge side of the space toward the tip side edge of the through-hole. a flow channel groove is formed in a surface of at least one of two resin substrates (10, 20); the two resin substrates (10, 20) are joined with a face facing inward where the flow channel groove is formed; in at least either one of the two resin substrates a through-hole of a circularly cross-sectional shape leading to the flow channel groove from a face of an opposite side to the face where the two resin substrates are joined is formed; and a space is formed in a joint face of the resin substrates in which the flow channel groove has been formed in one of the two resin substrates and the space has a depth (Tc) so as for a clearance to remain between the tip side edge of the through-hole and the joint face even when the two resin substrates (10, 20) are joined, in the face of the opposite side, a protrusion protruding in a thickness direction of the resin substrate is integrally formed with the resin substrate so as to surround the through-hole, characterized in that, the microchip in which the space having a circularly cross-sectional shape concentric with the through-hole and the depth in the same direction as the thickness direction of the resin substrate is formed on the joint face of at least one of the two resin substrates which is the joint face in the case where the protrusion is projected from a perpendicular direction to the joint face, when the tip side edge of the through-hole is projected on the joint face from the perpendicular direction, a relationship of φc > φa is satisfied and φa is larger than a width of the flow channel groove, provided that the diameter of the tip side edge of the through-hole is designated as φa and the diameter of the end edge side of the space making contact with the joint face is designated as φc,