Multi-functional rare-earth Yb(3+) and Ln(3+) (Ln = Er, Tm and Ho) ions doped one-dimensional (1-D) upconversion submicrocrystals (NaYF(4) and NaGdF(4)) possessing upconversion luminescence, biocompatibility and magnetic properties have been synthesized by a one-pot hydrothermal method. Rare-earth Yb(3+) and Ln(3+) ions doped NaYF(4) microrods (~1 μm in diameter, 3-5 μm in length) exhibit porous properties, and the average pore sizes are ~28.2 nm. They show paramagnetism in the magnetic range of -60 to -2 kOe and 2 to 60 kOe at 300 K, and exhibit near superparamagnetic behaviour at the magnetic range of -2 to 2 kOe. Saturation magnetization was ~12.1 emu g(-1) at 2 K. The Yb(3+) and Ln(3+) ions doped NaGdF(4) submicrocrystals (~100 nm in diameter, 200-300 nm in length) show paramagnetism at 300 K, and exhibit superparamagnetic behaviour with a saturation magnetization of 129.2 emu g(-1) at 2 K. The magnetic properties of Yb(3+) and Ln(3+) ions doped 1-D upconversion submicrocrystals indicate they can be used for drug targeting under a magnetic field. Their unique upconversion emission (green for Yb(3+)/Er(3+) and blue for Yb(3+)/Tm(3+)) under 980 nm laser excitation indicate that they could be used for specific luminescent immunolabeling and imaging. MTT assays reveal that 1-D upconversion submicrocrystals have satisfactory bio-affinity, where the viability keeps in good state even at a concentration of 500 μg mL(-1), which is much higher than the concentration usually used in cell labelling. Luminescent microscopy images show that the morphologies of the cytoskeleton and cell nucleus are well maintained after incubating different concentrations of 1-D upconversion submicrocrystals. After injecting upconversion submicrocrystals into the mice (tumor sites or back normal tissue), a clearly distinguished CT signal was observed, indicating the synthesized 1-D submicrocrystals are effective for CT imaging in vivo.