This thesis studies the intrinsic disorder effects and the transport and magnetic properties of ring-shaped epitaxial thin films and superconducting tunnel junctions (STJs) of the high temperature superconductor YBa$_2$Cu$_3$O$_{7-delta}$. We used an unconventional contactless technique that allows us to directly measure the persistent current of superconducting rings. In order to study the disorder effects on the persistent current, we slowly increased oxygen vacancies in YBa$_2$Cu$_3$O$_{7-delta}$ by changing $delta$ from 0.03 to 0.55 in steps of $sim$0.021. Monitoring the corresponding changes in the temperature dependence of the persistent current revealed an anomaly in its flow within a certain range of disorder. We found that this anomaly is directly related to the occurrence of a spinodal decomposition of oxygen vacancies in YBCO, which we explain as a competition between two coexisting phases, oxygen rich and oxygen deficient. The analysis of the time dependence of the persistent current revealed that increasing oxygen vacancies transforms the vortex structure from quasi-lattice into a glass and subsequently into a pinned liquid phase. Our results also exhibited the first evidence of self-organization of the vortex structure with increasing disorder. We also performed the first direct measurement of the temperature dependence of the $c$-axis persistent current ($J_c$) that is purely due to tunnelling Cooper-pairs through intrinsic Josephson junctions (IJJs) of YBCO. This is made possible by incorporating IJJs of YBCO into ring-shaped films. Then, we studied the temperature dependence of the persistent current of YBCO nanowires embedded in SrTiO$_3$-barrier integrated between two semi-ring-shaped YBCO thin films and systematically varied the nanowires length. Our observations revealed that $J_c$ has two different temperature dependences: a GL-dependence ($J_c propto (T_c - T)^{3/2}$) at low temperatures which we found the same in all studied samples, and another power law dependence ($J_c propto (T_c - T)^{alpha > 3/2}$) at high temperatures which turned out to depend on the length of the nanowires. We attribute the cross-over between these two temperature dependences to the depinning and the dissipative motion of vortices. These experimental approaches and findings not only provide new information, but more importantly open new avenues of investigating the transport and magnetic properties of superconducting films, junctions, and nanowires.

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