Asymmetric spindle pole body (SPB) inheritance requires a cascade of events that involve kinases, phosphatases and structural scaffold proteins including molecular motors and microtubule-associated proteins present in the nucleus and/or the cytoplasm. Higher levels of an SPB component Spc72 and the spindle positioning factor Kar9 at the old SPB, which migrates to the daughter cell, ensure asymmetric SPB inheritance. Timely SPB duplication followed by its asymmetric inheritance is a key to correct spindle alignment leading to high-fidelity chromosome segregation. By combining in silico analysis of known protein-protein interactions of autophagy (Atg)-related proteins with those that constitute the chromosome segregation machinery, and growth dynamics of 35 atg mutants in the presence of a microtubule poison, we identified Atg11 as a potential regulator of chromosome transmission. Cells lacking Atg11 did not show any kinetochore defects but displayed a high rate of chromosome loss and delayed anaphase onset. Atg11 positively interacted with Kar9 and Kip2 and negatively with Dyn1 and Kar3 in mediating proper chromosome segregation suggesting a role of Atg11 in spindle positioning. Indeed, atg11∆ cells displayed an inverted SPB inheritance. We further show that Atg11 promotes asymmetric localization of Spc72 and Kar9 on the old SPB. Atg11 physically interacted with Spc72 and transiently localized close to the old SPB during metaphase-to-anaphase progression. Taken together, our study uncovers an autophagy-independent role of Atg11 in spindle alignment and emphasizes the importance of unbiased screens to identify factors mediating the complex and intricate crosstalk between processes fundamental to genomic integrity.Significance statementDysregulation in spindle alignment during cell division causes decreased lifespan and contributes to diseased states related to aneuploidy such as cancer. The alignment of the mitotic spindle along the mother-bud axis in the budding yeast relies on the differential distribution of proteins between existing old and freshly formed new spindle pole bodies (SPBs). Non-random distribution of Spc72 and Kar9 facilitates the asymmetric inheritance of SPBs, vital for proper spindle elongation and alignment. Here, we identified a non-canonical role of an autophagy-related protein Atg11 in the Kar9-mediated spindle positioning and faithful chromosome segregation. Loss of Atg11 leads to randomized Spc72 distribution. Atg11, like other autophagy proteins, is evolutionarily conserved. Thus, this study reiterates the importance of crosstalk among major biological processes.